openmolecules.org Forum: Functionality

Home » DataWarrior » Functionality » PCA (loading_plots)

Show: Today's Messages :: Polls :: Message Navigator

PCA [message #360]

Tue, 19 June 2018 22:09

khom
Messages: 9
Registered: April 2018

Junior Member

Could you please tell me how I could get access to the loading plot of a PCA analysis? Thank you.

Report message to a moderator

Re: PCA [message #362 is a reply to message #360]

Sun, 08 July 2018 18:33

thomas
Messages: 729
Registered: June 2014

Senior Member

I am not sure, whether I understand your question correctly. If you intend to make a PCA from multidimensional data and then plot the 2 or 3 most significant dimensions, then you need to do these steps:

- Data-> Calculate Principal Components...
- select the columns that contain your input data (or a descriptor column of chemical structures)
- click OK

Does this answer your question?

Thomas

Report message to a moderator

Re: PCA [message #365 is a reply to message #362]

Tue, 10 July 2018 20:43

khom
Messages: 9
Registered: April 2018

Junior Member

Thomas,
I am sorry that I did not pose my question clearly. The PCA plots (PC1 vs PC2, for example) generated as per your instructions are the scores, describing the relations among the observations (samples, rows); I am trying to see if the corresponding loadings plots describing the relationships among the variables (columns) can be displayed as well. Thank you.
Kellie

Report message to a moderator

Re: PCA [message #366 is a reply to message #365]

Wed, 11 July 2018 12:57

thomas
Messages: 729
Registered: June 2014

Senior Member

Kellie,
thank you for clarifying. Currently the linear contribution factors (loadings) of the original dimensions are just used internally. One could think of adding a button that allows to copy them as a new table into the clipboard. A paste operation would then create a new DataWarrior file allowing to depict the contributions.
Thomas

Report message to a moderator

Re: PCA [message #367 is a reply to message #366]

Wed, 11 July 2018 15:30

thomas
Messages: 729
Registered: June 2014

Senior Member

A small update: I just added a checkbox in the PCA dialog that allows to open an additional window after PCA calculation showing a table with the originally selected variables in rows and their Eigen values in columns. Plots of scores and loadings are equivalent to this example: https://learnche.org/pid/latent-variable-modelling/principal -component-analysis/interpreting-score-plots-and-loading-plo ts

Thus, the next version will have it.

Thomas

Report message to a moderator

Re: PCA [message #368 is a reply to message #367]

Wed, 11 July 2018 19:49

khom
Messages: 9
Registered: April 2018

Junior Member

Thomas,
Thank you very much indeed!! The info from the link are very useful also.
Kellie

Report message to a moderator

Previous Topic:	How to enter custom core?
Next Topic:	chEMBL structure download limit ?

Goto Forum:

-=] Back to Top [=-

[ Syndicate this forum (XML) ] [

] [

]

Current Time: Sat Apr 12 16:09:43 CEST 2025

Total time taken to generate the page: 0.03122 seconds